Variant report

Variant	esv3504235
Chromosome Location	chr19:56644842-56645235
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:56642703..56647128-chr19:56651543..56655262,4	MCF-7	breast:
2	chr19:56632432..56634662-chr19:56644261..56647544,4	MCF-7	breast:
3	chr19:56637204..56640116-chr19:56644041..56647745,4	K562	blood:
4	chr19:56644274..56647215-chr19:56650542..56653019,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167685	chromatin interactions
ENSG00000142409	chromatin interactions

Extended variants
information (count: 25 )
Associated
traits (count: 65 )

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs662308	chr19:56644842-56644843	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs533814395	chr19:56644867-56644868	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs372732906	chr19:56644908-56644909	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs576918166	chr19:56644910-56644911	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs565879	chr19:56644911-56644912	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs562384498	chr19:56644917-56644918	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs571360739	chr19:56644939-56644940	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs536774073	chr19:56644940-56644941	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs541558372	chr19:56644948-56644949	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs561312917	chr19:56644959-56644960	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs527302745	chr19:56644964-56644965	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs557102806	chr19:56644969-56644970	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs564808394	chr19:56645039-56645040	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs533493286	chr19:56645044-56645045	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs142690294	chr19:56645075-56645076	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs189670760	chr19:56645106-56645107	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs2637093	chr19:56645131-56645132	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs186920895	chr19:56645139-56645140	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs370010417	chr19:56645181-56645182	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs67187542	chr19:56645182-56645183	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs55639822	chr19:56645196-56645197	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs548679877	chr19:56645213-56645214	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs368253776	chr19:56645217-56645218	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs115412164	chr19:56645227-56645228	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs192177688	chr19:56645231-56645232	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:65)

Disease	PMID	Source
Myelodysplastic syndrome	17634407	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Cancer	21637783	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Ovarian cancer	21720365	CNVD
Cancer	20164919	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Ductal carcinoma	22052326	CNVD
Congenital nephrotic syndrome	18421352	CNVD
Astrocytoma	17934521	CNVD
Leukemia	17361228	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Breast cancer	17603634	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Endometrial cancer	22040021	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Oligodendroglial tumors	17285580	CNVD
renal disease	20603712	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Chordoma	18071362	CNVD
Urothelial carcinoma	21177765	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	16864856	CNVD
Bladder cancer	21909424	CNVD
Medulloblastoma	16783165	CNVD
Acute myeloid leukemia	20729466	CNVD
Ovarian cancer	22174824	CNVD
Multiple myeloma	16616336	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Wilms tumour	21544195	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Congenital anomalies of the kidney and urinary tract	18852474	CNVD
Glioblastoma multiforme	17002787	CNVD
Cervical cancer	21062161	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Prostate cancer	16573809	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Lung cancer	18438408	CNVD
Colorectal cancer	16272173	CNVD
Ovarian cancer	21781307	CNVD
Neuroblastoma	20406844	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Alzheimer''s disease	22166940	CNVD
Heart disease	21282601	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Glioblastoma multiforme	21922591	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Breast cancer	20409316	CNVD

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56634000-56645400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr19:56637400-56645400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr19:56637800-56645200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr19:56637800-56647600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:56638600-56651200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr19:56638800-56651800	Weak transcription	Spleen	Spleen
7	chr19:56639000-56647600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:56639200-56645200	Weak transcription	K562	blood
9	chr19:56639200-56645600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr19:56640800-56649000	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr19:56642600-56647800	Enhancers	Placenta	Placenta
12	chr19:56643200-56645000	Enhancers	Ovary	ovary
13	chr19:56643200-56645800	Enhancers	Fetal Muscle Trunk	muscle
14	chr19:56643600-56646200	Enhancers	Primary B cells from cord blood	blood
15	chr19:56643800-56645400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:56644000-56645200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr19:56644000-56645400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr19:56644000-56651200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr19:56644000-56651200	Weak transcription	Lung	lung
20	chr19:56644000-56651200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr19:56644200-56645000	Enhancers	Stomach Smooth Muscle	stomach
22	chr19:56644200-56645200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr19:56644200-56645200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr19:56644200-56645200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:56644200-56645200	Weak transcription	HSMMtube	muscle
26	chr19:56644200-56645200	Weak transcription	NH-A	brain
27	chr19:56644200-56645400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr19:56644200-56645400	Weak transcription	HepG2	liver
29	chr19:56644200-56645400	Weak transcription	HSMM	muscle
30	chr19:56644200-56645600	Weak transcription	Fetal Muscle Leg	muscle
31	chr19:56644200-56645800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr19:56644200-56646000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr19:56644200-56646000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr19:56644200-56646000	Enhancers	Osteobl	bone
35	chr19:56644200-56646800	Weak transcription	Liver	Liver
36	chr19:56644200-56647600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:56644200-56647600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr19:56644200-56647600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr19:56644200-56647600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr19:56644200-56647600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:56644200-56649400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr19:56644200-56651200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr19:56644200-56651200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr19:56644200-56651200	Weak transcription	Brain Anterior Caudate	brain
45	chr19:56644200-56651200	Weak transcription	Fetal Kidney	kidney
46	chr19:56644200-56651400	Weak transcription	Right Atrium	heart
47	chr19:56644400-56645600	Weak transcription	Fetal Stomach	stomach
48	chr19:56644400-56651200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr19:56644600-56645000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:56644600-56645000	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links